3-148997054-TTGTGTGTGTGTGTG-TTGTGTGTGTGTGTGTGTGTGTG
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2
The NM_004130.4(GYG1):c.481+172_481+179dupGTGTGTGT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0214 in 606,362 control chromosomes in the GnomAD database, including 105 homozygotes. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.028 ( 73 hom., cov: 0)
Exomes 𝑓: 0.019 ( 32 hom. )
Consequence
GYG1
NM_004130.4 intron
NM_004130.4 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.285
Genes affected
GYG1 (HGNC:4699): (glycogenin 1) This gene encodes a member of the glycogenin family. Glycogenin is a glycosyltransferase that catalyzes the formation of a short glucose polymer from uridine diphosphate glucose in an autoglucosylation reaction. This reaction is followed by elongation and branching of the polymer, catalyzed by glycogen synthase and branching enzyme, to form glycogen. This gene is expressed in muscle and other tissues. Mutations in this gene result in glycogen storage disease XV. This gene has pseudogenes on chromosomes 1, 8 and 13 respectively. Alternatively spliced transcript variants encoding different isoforms have been identified.[provided by RefSeq, Sep 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP6
Variant 3-148997054-T-TTGTGTGTG is Benign according to our data. Variant chr3-148997054-T-TTGTGTGTG is described in ClinVar as [Likely_benign]. Clinvar id is 1196791.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0276 (4137/149796) while in subpopulation AFR AF= 0.0408 (1656/40614). AF 95% confidence interval is 0.0391. There are 73 homozygotes in gnomad4. There are 2071 alleles in male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 73 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GYG1 | NM_004130.4 | c.481+172_481+179dupGTGTGTGT | intron_variant | ENST00000345003.9 | NP_004121.2 | |||
GYG1 | NM_001184720.2 | c.481+172_481+179dupGTGTGTGT | intron_variant | NP_001171649.1 | ||||
GYG1 | NM_001184721.2 | c.481+172_481+179dupGTGTGTGT | intron_variant | NP_001171650.1 | ||||
GYG1 | XM_017006275.2 | c.304+172_304+179dupGTGTGTGT | intron_variant | XP_016861764.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GYG1 | ENST00000345003.9 | c.481+150_481+151insTGTGTGTG | intron_variant | 1 | NM_004130.4 | ENSP00000340736.4 |
Frequencies
GnomAD3 genomes AF: 0.0276 AC: 4130AN: 149680Hom.: 72 Cov.: 0
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GnomAD4 exome AF: 0.0194 AC: 8861AN: 456566Hom.: 32 AF XY: 0.0199 AC XY: 4843AN XY: 243632
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GnomAD4 genome AF: 0.0276 AC: 4137AN: 149796Hom.: 73 Cov.: 0 AF XY: 0.0283 AC XY: 2071AN XY: 73086
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Apr 13, 2020 | - - |
Computational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at